Zinc coordination sphere in biochemical zinc sites

Abstract

Zinc is known to be indispensable to growth and development and transmission of the genetic message. It does this through a remarkable mosaic of zinc binding motifs that orchestrate all aspects of metabolism. There are now nearly 200 three dimensional structures for zinc proteins, representing all six classes of enzymes and covering a wide range of phyla and species. These structures provide standards of reference for the identity and nature of zinc ligands in other proteins for which only the primary structure is known. Three primary types of zinc sites are apparent from examination of these structures: structural, catalytic and cocatalytic. The most common amino acids that supply ligands to these sites are His, Glu, Asp and Cys. In catalytic sites zinc generally forms complexes with water and any three nitrogen, oxygen and sulfur donors with His being the predominant amino acid chosen. Water is always a ligand to such sites. Structural zinc sites have four protein ligands and no bound water molecule. Cys is the preferred ligand in such sites. Cocatalytic sites contain two or three metals in close proximity with two of the metals bridged by a side chain moiety of a single amino acid residue, such as Asp, Glu or His and sometimes a water molecule. Asp and His are the preferred amino acids for these sites. No Cys ligands are found in such sites. The scaffolding of the zinc sites is also important to the function and reactivity of the bound metal. The influence of zinc on quaternary protein structure has led to the identification of a fourth type of zinc binding site, protein interface. In this case zinc sites are formed from ligands supplied from amino acid residues residing in the binding surface of two proteins. The resulting zinc site usually has the coordination properties of a catalytic or structural zinc binding site.Abbreviations: ABC -ATP-binding cassette; AAP -Aeromonas proteolytica aminopeptidase; ADAadenosine deaminase; ADAM -A disintegrin and metalloprotease domain; ADH -alcohol dehydrogenase; ALA-5-aminolevulinic acid; ALAD-5-aminolevulinic acid dehydratase; Apo2L or TRAIL-apoptosis-inducing ligand 2; BIR-baculovirus inhibitor of apoptosis repeat; BLAP-bovine lens leucine aminopeptidase; CA-carbonic anhydrase; CAM-y-carbonic anhydrase; CPD A-carboxypeptidase A; CDA-cytidine deaminase; EDTA -ethylenediaminetetraacetic acid; eNOS or NOS-3-endothelial nitric oxide synthase; FPP-farnesyl diphosphate; FTase -farnesyl transferase; H4B -tetrahydrobiopterin; HIV -human immunodeficiency virus; GGPPgeranylgeranyl diphosphate; GSNO-S-nitrosoglutathione; HLA-DR-class II major histocompatibility molecule; huiFN-human interferon; lAP-inhibitor of apoptosis; iNOS or NOS-2 -inducible nitric oxide synthase; Im3 -E. coli immunity protein; IUB -International Union of Biochemistry; MEROPS -system for classification of peptidase sequences; MetAP-1 -methionine aminopeptidase-); MetAP-2 -methionine aminopeptidase-2; MHC-major histocompatibility complex; MMP-matrix metalloproteinase; MPD-2-methyl-2,4-pentanediol; NAD...

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